Integrative single-cell spatial genomic, transcriptomic, and epigenetic imaging in mammalian tissue

项目摘要/摘要 基因组的三维(3D)组织影响许多基因组功能。多个3D基因组 不同长度比例的体系结构，包括染色质循环、区域、隔间和区域 与核膜和核仁有关，已经发现。这些架构中的更改已经 与正常发育、衰老和多种疾病有关。然而，这些结构是如何 在同一细胞中排列，它们在哺乳动物组织中的不同细胞类型中如何变化，以及它们是如何 与基因表达相关的基因和组织中的表观基因组在很大程度上是未知的。当前 由于缺乏同时追踪染色质折叠的能力 长度标尺，测量基因组组织与其他核成分的关系，以及剖面基因 在哺乳动物组织中的同一单个细胞中的表达和表观基因组。为了满足这一需求，我们在这里 建议开发一种新的方法，称为核组结构的多重成像(MINA)，该方法 将能够同时测量多尺度染色质折叠，基因组区域与 核层、核仁和其他核/表观遗传成分，以及大量RNA的拷贝数 同一物种，哺乳动物组织中的单个细胞。我们预计这一发展将广泛影响许多 通过描绘相关的细胞类型特定的多尺度基因组结构来研究3D基因组学 通过基因表达和表观基因组，在不同类型的组织中经历不同的生物过程。 此外，通过允许在同一单元内进行测量，将来将有可能直接测试 基因组结构和基因表达之间的因果关系，从而打开了一个全新的 识别调节人类基因表达的新机制的实验范式 发展、健康和疾病。

Project Summary/Abstract The three-dimensional (3D) organization of the genome affects many genomic functions. Multiple 3D genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. Changes in these architectures have been associated with normal development, aging, and a wide range of diseases. However, how these structures are arranged in the same cell, how they vary in different cell types in mammalian tissue, and how they are correlated with gene expression and the epigenome in the tissue contexts are largely unknown. Current approaches are severely limited by a lack of capacity to simultaneously trace chromatin folding across multiple length scales, measure genomic organization in relation to other nuclear components, and profile gene expression and epigenome in the same single cells in mammalian tissue. To address this need, here we propose to develop a new methodology, termed Multiplexed Imaging of Nucleome Architectures (MINA), which will enable simultaneous measurements of multiscale chromatin folding, associations of genomic regions with nuclear lamina, nucleoli and other nuclear/epigenetic components, and copy numbers of numerous RNA species in the same, single cells in mammalian tissue. We expect this development to broadly impact many lines of research on 3D genomics by depicting cell-type-specific multiscale genomic architectures associated with gene expression and epigenome, in different types of tissue undergoing different biological processes. Furthermore, by allowing measurements within the same cell, it will in future be possible to directly test the causal relationship between genomic architecture and gene expression, thus opening up a completely new experimental paradigm to identify novel mechanisms that regulate gene expression across human development, health and disease.